Malleable Molecular Dynamics Simulations with GROMACS and DMR

TL;DR

This paper introduces a malleable version of GROMACS that dynamically adjusts MPI processes during simulations, improving resource utilization and reducing costs on HPC systems.

Contribution

It integrates DMR middleware with GROMACS to enable MPI process malleability, a novel approach for efficient, adaptive molecular dynamics simulations.

Findings

Dynamic GROMACS reduces idle resources and queue delays.

Reconfiguration overheads are minimal compared to gains.

Significant node-hour savings observed on MareNostrum 5.

Abstract

Static resource allocations in high-performance computing (HPC) lead to inefficiencies for time-varying workloads, causing idle resources, queue delays, and higher node-hour costs. The Dynamic Management of Resources (DMR) middleware enables MPI process malleability in Slurm via a simple API decoupled from scheduler internals. In this work, we integrate DMR into the GROMACS molecular dynamics engine to obtain a malleable variant that can dynamically adapt its MPI process count by combining communication-efficiency-aware reconfiguration with GROMACS' native checkpoint/restart mechanism. We evaluate this design on the MareNostrum~5 supercomputer, comparing dynamic runs against static executions and quantifying reconfiguration overheads, time-to-solution, and node-hour savings for bursty GROMACS workloads.